Behavior of the bacterial flagellar motor depends sensitively on the external loads it drives. Motor switching, which provides the basis for the run-and-tumble behavior of flagellated bacteria, has been studied for motors under zero to high loads, revealing a nonequilibrium effect that is proportional to the motor torque. However, behavior of the motor switching at stall (with maximum torque) remains unclear. An extrapolation from previous studies would suggest the maximum nonequilibrium effect for motor switching at stall. Here, we stalled the motor using optical tweezers and studied the motor switching with a high time resolution of about 2 ms. Surprisingly, our results showed exponentially distributed counterclockwise (CCW) and clockwise (CW) intervals, indicating that motor switching at stall is probably an equilibrium process. Combined with previous experiments at other loads, our result suggested that the nonequilibrium effect in motor switching arises from the asymmetry of the torque generation in the CCW and CW directions. By including this nonequilibrium effect in the general Ising-type conformation spread model of the flagellar switch, we consistently explained the motor switching over the whole range of load conditions. We expect to see a similar mechanism of nonequilibrium regulation in other molecular machines.

Living many-body systems often exhibit scale-free collective behavior reminiscent of thermal critical phenomena. But their mutual interactions are inevitably retarded due to information processing and delayed actuation. We numerically investigate the consequences for the finite-size scaling in the Vicsek model of motile active matter. A growing delay time initially facilitates but ultimately impedes collective ordering and turns the dynamical scaling from diffusive to ballistic. It provides an alternative explanation of swarm traits previously attributed to inertia.

We consider the yielding behavior of amorphous solids under cyclic shear deformation and show that it can be mapped into a random walk in a confining potential with an absorbing boundary. The resulting dynamics is governed by the first passage time into the absorbing state and suffices to capture the essential qualitative features recently observed in atomistic simulations of amorphous solids. Our results provide insight into the mechanism underlying yielding and its robustness. When the possibility of activated escape from absorbing states is added, it leads to a unique determination of a threshold energy and yield strain, suggesting thereby an appealing approach to understanding fatigue failure.

The swelling dynamics of polymer gels are characterized by the (collective) diffusion coefficient $D$ of the polymer network. Here, we measure the temperature dependence of $D$ of polymer gels with controlled homogeneous network structures using dynamic light scattering. An evaluation of the diffusion coefficient at the gelation point $D_{\mathrm{gel}}$ and the increase therein as the gelation proceeds $\mathrm{\Delta }D\equiv D-D_{\mathrm{gel}}$ indicates that $\mathrm{\Delta }D$ is a linear function of the absolute temperature with a significantly large negative constant term. This feature is formally identical to the recently discovered “negative energy elasticity” [Y. Yoshikawa et al. Phys. Rev. X 11, 011045 (2021)], demonstrating a nontrivial similarity between the statics and dynamics of polymer networks.

We investigate the susceptibility of long-range ordered phases of two-dimensional dry aligning active matter to population disorder, taken in the form of a distribution of intrinsic individual chiralities. Using a combination of particle-level models and hydrodynamic theories derived from them, we show that while in finite systems all ordered phases resist a finite amount of such chirality disorder, the homogeneous ones (polar flocks and active nematics) are unstable to any amount of disorder in the infinite-size limit. On the other hand, we find that the inhomogeneous solutions of the coexistence phase (bands) may resist a finite amount of chirality disorder even asymptotically.

We develop a constitutive model allowing for the description of the rheology of two-dimensional soft dense suspensions above jamming. Starting from a statistical description of the particle dynamics, we derive, using a set of approximations, a nonlinear tensorial evolution equation linking the deviatoric part of the stress tensor to the strain-rate and vorticity tensors. The coefficients appearing in this equation can be expressed in terms of the packing fraction and of particle-level parameters. This constitutive equation rooted in the microscopic dynamic qualitatively reproduces a number of salient features of the rheology of jammed soft suspensions, including the presence of yield stresses for the shear component of the stress and for the normal stress difference. More complex protocols like the relaxation after a preshear are also considered, showing a smaller stress after relaxation for a stronger preshear.

We study the elastocapillary interaction between flexible microfibers in contact with bubbles trapped at the surface of a liquid bath. Microfibers placed on top of bubbles are found to migrate to and wrap into a coil around the perimeter of the bubble for certain bubble-fiber size combinations. The wrapping process is spontaneous: the coil spins atop the bubble, thereby drawing in excess fiber floating on the bath. A two-dimensional microfiber coil emerges which increases the lifetime of the bubbles. A simple model incorporating surface and bending energies captures the spontaneous winding process.

A key question in evolution is how likely a mutant is to take over. This depends on natural selection and on stochastic fluctuations. Population spatial structure can impact mutant fixation probabilities. We introduce a model for structured populations on graphs that generalizes previous ones by making migrations independent of birth and death. We demonstrate that by tuning migration asymmetry, the star graph transitions from amplifying to suppressing natural selection. The results from our model are universal in the sense that they do not hinge on a modeling choice of microscopic dynamics or update rules. Instead, they depend on migration asymmetry, which can be experimentally tuned and measured.

Transcription of genes can be affected by both biochemical and mechanical factors. Recent experiments suggested that the mechanical stress associated with transcription-induced DNA supercoiling is responsible for the transition from cooperative to antagonistic group dynamics of RNA polymerases (RNAPs) upon promoter repression. To underpin the mechanism behind this drastic transition, we developed a continuum deterministic model for transcription under torsion. In our model, the speed of an RNAP is affected by the local DNA supercoiling, as well as two global factors: (i) the number of RNAPs on the gene affecting the torsional stress experienced by individual RNAPs and (ii) transcription factors blocking the diffusion of DNA supercoils. Our minimal model can successfully reproduce the experimental findings and helps elucidate the interplay of mechanical and biological factors in the collective dynamics of molecular machines involved in gene expression.

We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is driven by stochastic steps along a biased chemical free energy landscape. We find conditions under which the enzymes can synchronize their catalytic steps, and discover that the coupling can lead to a significant enhancement in their overall catalytic rate. Both effects can be understood as arising from a global bifurcation in the underlying dynamical system at sufficiently strong coupling. Our findings suggest that, despite their molecular scale, enzymes can be cooperative and improve their performance in metabolic clusters.